First and foremost, it's almost definitely fine! The point here isn't to totally get rid of <div>s, it's to stop using them in cases where they have some semantic meaning that's covered by another element. But generic containers with no semantics to them are exactly what <div>s are, so if they're just grouping things for styling purposes, not semantic purposes, you're all good!

Second, with the above said, as kind of a side comment, if you're creating a lot of nested flex containers, you probably would be better served with a flatter HTML structure and CSS Grid for the layout. Grid is supported pretty solidly at this point, and it's usually not hard to create fallbacks for older browsers that still look perfectly fine (even if they don't exactly match the mockup) without adding any extra markup. If you haven't tried Grid yet, give it a shot, it'll blow your mind! (If you can't tell, I'm very excited about Grid, I wrote a couple article about how pumped I am haha, I recommend this one you wanna see the thing I love most)

If the only reason you aren't using CSS Grid yet is because IE11 needs to look identical; I wrote a whole series on how to write modern CSS Grid code that works perfectly in IE with no fallback styles.